A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2

Cell Signal. 2014 Jun;26(6):1243-57. doi: 10.1016/j.cellsig.2014.02.011. Epub 2014 Feb 28.


Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function. A new linear motif based on a MDM2 interaction consensus is used to select novel MDM2 interactors based on Nutlin-3 responsiveness in a cell-based proteomics screen. MDM2 binds a subset of peptide motifs corresponding to real proteins with a range of allosteric responses to MDM2 ligands. We validate cyclophilin B as a novel protein with a consensus MDM2 binding motif that is stabilised by Nutlin-3 in vivo, thus identifying one of the few known interactors of MDM2 that is stabilised by Nutlin-3. These data invoke two modes of peptide binding at the MDM2 N-terminus that rely on a consensus core motif to control the equilibrium between MDM2 binding proteins. This approach stratifies MDM2 interacting proteins based on the linear motif feature and provides a new biomarker assay to define clinically relevant Nutlin-3 responsive MDM2 interactors.

Keywords: CypB; Interactome; Linear motifs; MDM2; Proteomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding, Competitive
  • Consensus Sequence
  • Cyclophilins / metabolism*
  • Humans
  • Imidazoles / pharmacology
  • MCF-7 Cells
  • Models, Molecular
  • Molecular Sequence Data
  • Piperazines / pharmacology
  • Protein Binding
  • Protein Denaturation
  • Protein Interaction Domains and Motifs
  • Protein Interaction Mapping
  • Protein Interaction Maps
  • Proto-Oncogene Proteins c-mdm2 / antagonists & inhibitors
  • Proto-Oncogene Proteins c-mdm2 / metabolism*


  • Imidazoles
  • Piperazines
  • cyclophilin B
  • nutlin 3
  • MDM2 protein, human
  • Proto-Oncogene Proteins c-mdm2
  • Cyclophilins